Methods for semi-automated index generation for high precision information retrieval

.............................................................................................................................. v Acknowledgements ...........................................................................................................vii List of Tables..................................................................................................................... xv List of Figures .................................................................................................................xvii Chapter 1: Introduction ....................................................................................................... 1 1.1 The Nature of Medical Information ........................................................................ 2 1.2 Clinicians’ Information Needs ................................................................................ 3 1.3 Evaluation of Indexes of Medical Information through Information Retrieval system Performance ................................................................................................ 4 1.4 High-precision Information Indexing and Retrieval ............................................... 6 1.5 Internet-based Semi-automated Indexing of Documents ...................................... 10 1.6 An ISAID Indexing Example ................................................................................ 14 1.7 Evaluation of the ISAID system............................................................................ 15 1.8 Guide to the Dissertation....................................................................................... 16 Chapter 2: Access to Medical Information ....................................................................... 19 2.1 Evaluation of Information Retrieval Systems ....................................................... 20 2.2 Indexing and Retrieval by Document Keyword.................................................... 22 2.2.1 Searching the MEDLINE Index ................................................................... 23 2.2.2 Limitations of Search-Accuracy with Keyword Indexing ........................... 29 2.3 Alternative Approaches to Medical-Information Indexing and Retrieval............. 30 2.3.1 Word-Statistical Systems ............................................................................. 31 2.3.2 Linguistic Information-Retrieval Systems ................................................... 34 2.3.3 Knowledge-Based Systems .......................................................................... 35 2.3.3.1 Context-Model–Based Systems .......................................................... 36 2.3.3.2 Knowledge-Based Query Formulation................................................ 39

[1]  W. Hersh Information Retrieval: A Health Care Perspective , 1995, Computers and Medicine.

[2]  B. Buchanan,et al.  Expanding the concept of medical information: an observational study of physicians' information needs. , 1992, Computers and biomedical research, an international journal.

[3]  Estelle Brodman,et al.  Evaluation of the MEDLARS Demand Search Service , 1969 .

[4]  David Fisher,et al.  Description of the UMass system as used for MUC-6 , 1995, MUC.

[5]  Lawrence M. Fagan,et al.  MYCIN II: design and implementation of a therapy reference with complex content-based indexing , 1998, AMIA.

[6]  J J Cimino,et al.  Generating MEDLINE search strategies using a librarian knowledge-based system. , 1993, Proceedings. Symposium on Computer Applications in Medical Care.

[7]  David Fisher,et al.  MITA: An Information-Extraction Approach to the Analysis of Free-Form Text in Life Insurance Applications , 1998, AI Mag..

[8]  W R Hersh,et al.  A Comparison of Two Methods for Indexing and Retrieval from a Full-text Medical Database , 1992, Medical decision making : an international journal of the Society for Medical Decision Making.

[9]  Y Yang,et al.  An evaluation of statistical approaches to MEDLINE indexing. , 1996, Proceedings : a conference of the American Medical Informatics Association. AMIA Fall Symposium.

[10]  Carol Friedman,et al.  Identification of findings suspicious for breast cancer based on natural language processing of mammogram reports , 1997, AMIA.

[11]  K. A. McKibbon,et al.  Online access to medline in clinical settings , 2020 .

[12]  John F. Sowa Conceptual Graph Standard and Extension , 1998, ICCS.

[13]  James R. Cowie,et al.  Automatic Analysis of Descriptive Texts , 1983, ANLP.

[14]  Ellen Riloff,et al.  Automatically Constructing a Dictionary for Information Extraction Tasks , 1993, AAAI.

[15]  Michael F. Lynch,et al.  Extraction of Information from the Text of Chemical Patents. 1. Identification of Specific Chemical Names , 1998, J. Chem. Inf. Comput. Sci..

[16]  Alan R. Aronson,et al.  Exploiting a Large Thesaurus for Information Retrieval , 1994, RIAO.

[17]  G. Rongen The Washington Manual of Medical Therapeutics , 2002 .

[18]  C A Bachrach,et al.  Selection of MEDLINE contents, the development of its thesaurus, and the indexing process. , 1978, Medical informatics = Medecine et informatique.

[19]  E. Riloff,et al.  Automated dictionary construction for information extraction from text , 1993, Proceedings of 9th IEEE Conference on Artificial Intelligence for Applications.

[20]  Terry Winograd,et al.  Understanding computers and cognition , 1986 .

[21]  Olivier Bodenreider,et al.  Beyond synonymy: exploiting the UMLS semantics in mapping vocabularies , 1998, AMIA.

[22]  W. DuMouchel,et al.  Unlocking Clinical Data from Narrative Reports: A Study of Natural Language Processing , 1995, Annals of Internal Medicine.

[23]  Martin F. Porter,et al.  An algorithm for suffix stripping , 1997, Program.

[24]  Penelope Sibun,et al.  A Practical Part-of-Speech Tagger , 1992, ANLP.

[25]  R A Greenes,et al.  SAPHIRE--an information retrieval system featuring concept matching, automatic indexing, probabilistic retrieval, and hierarchical relationships. , 1990, Computers and biomedical research, an international journal.

[26]  George Hripcsak,et al.  Automating a severity score guideline for community-acquired pneumonia employing medical language processing of discharge summaries , 1999, AMIA.

[27]  G. Zipf,et al.  Relative Frequency as a Determinant of Phonetic Change , 1930 .

[28]  W. G. Cole,et al.  Metaphrase: An Aid to the Clinical Conceptualization and Formalization of Patient Problems in Healthcare Enterprises , 1998, Methods of Information in Medicine.

[29]  Mark Alan Musen Generation of model-based knowledge-acquisition tools for clinical-trial advice systems , 1988 .

[30]  Douglas E. Appelt,et al.  FASTUS: A Finite-state Processor for Information Extraction from Real-world Text , 1993, IJCAI.

[31]  Lee Goldman,et al.  Cecil Textbook of Medicine , 1985 .

[32]  T. Takagi,et al.  Toward information extraction: identifying protein names from biological papers. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[33]  Hans Paijmans Comparing the document representations of two IR-systems: CLARIT and TOPIC , 1993 .

[34]  N Sager,et al.  Automatic encoding into SNOMED III: a preliminary investigation. , 1994, Proceedings. Symposium on Computer Applications in Medical Care.

[35]  David Fisher,et al.  Issues in inductive learning of domain-specific text extraction rules , 1995, Learning for Natural Language Processing.

[36]  Susanne M. Humphrey Indexing biomedical documents: From thesaural to knowledge-based retrieval systems , 1992, Artif. Intell. Medicine.

[37]  David Fisher,et al.  CRYSTAL: Inducing a Conceptual Dictionary , 1995, IJCAI.

[38]  W R Hersh,et al.  A comparison of retrieval effectiveness for three methods of indexing medical literature. , 1992, The American journal of the medical sciences.

[39]  Gian Piero Zarri,et al.  Automatic Representation of the Semantic Relationships Corresponding to a French Surface Expression , 1983, ANLP.

[40]  Lawrence M. Fagan,et al.  Automated Text Markup for Information Retrieval from an Electronic Textbook of Infectious Disease , 1998, AMIA.

[41]  Denise R. Aberle,et al.  Extracting information from free text radiology reports , 1997, International Journal on Digital Libraries.

[42]  John F. Sowa,et al.  Conceptual graphs as a universal knowledge representation , 1992 .

[43]  K. Shimokata,et al.  Involvement of interleukin-8 in dialysis-related arthritis. , 1998, Kidney international.

[44]  M. Murray,et al.  Acute and Chronic Effects of Nonsteroidal Antiinflammatory Drugs on Glomerular Filtration Rate in Elderly Patients , 1995, The American journal of the medical sciences.

[45]  Stephen Soderland CRYSTAL: Learning Domain-specic Text Analysis Rules , 1996 .

[46]  L A Lenert,et al.  Monitoring free-text data using medical language processing. , 1993, Computers and biomedical research, an international journal.

[47]  Lawrence M. Fagan,et al.  Knowledge requirements for automated inference of medical textbook markup , 1999, AMIA.

[48]  J Starren,et al.  Architectural requirements for a multipurpose natural language processor in the clinical environment. , 1995, Proceedings. Symposium on Computer Applications in Medical Care.

[49]  Stefan Decker,et al.  Creating Semantic Web Contents with Protégé-2000 , 2001, IEEE Intell. Syst..

[50]  Claire Cardie,et al.  Evaluating an Information Extraction System , 1994 .

[51]  Tamas E. Doszkocs,et al.  An Associative Semantic Network for Machine-Aided Indexing, Classification and Searching , 1992 .

[52]  George A. Miller,et al.  WordNet: A Lexical Database for English , 1995, HLT.

[53]  M E Funk,et al.  Indexing consistency in MEDLINE. , 1983, Bulletin of the Medical Library Association.

[54]  Alexa T. McCray,et al.  Research Paper: Evaluating the Coverage of Controlled Health Data Terminologies: Report on the Results of the NLM/AHCPR Large Scale Vocabulary Test , 1997, J. Am. Medical Informatics Assoc..

[55]  Susanne M. Humphrey Interactive Knowledge-Based Indexing : The MedlndEx System , 1988, RIAO.

[56]  Olivier Bodenreider,et al.  The NLM Indexing Initiative , 2000, AMIA.

[57]  Thomas C. Rindflesch,et al.  Query Expansion Using the UMLS ® Metathesaurus ® , 1997 .

[58]  Ralph Grishman,et al.  COMLEX Syntax – A Large Syntactic Dictionary for Natural Language Processing , 1997, Comput. Humanit..

[59]  Carol Friedman,et al.  A broad-coverage natural language processing system , 2000, AMIA.

[60]  M. Resnick,et al.  Surgery of the Prostate , 1997 .

[61]  Gerard Salton,et al.  A Comparison Between Manual and Automatic Indexing Methods , 1968 .

[62]  Karen Spärck Jones,et al.  Natural language processing for information retrieval , 1996, CACM.

[63]  David R. Karger,et al.  Scatter/Gather as a Tool for the Navigation of Retrieval Results , 1995 .

[64]  G W Moore,et al.  Performance analysis of manual and automated systemized nomenclature of medicine (SNOMED) coding. , 1994, American journal of clinical pathology.

[65]  Mark A. Musen,et al.  The Knowledge Model of Protégé-2000: Combining Interoperability and Flexibility , 2000, EKAW.

[66]  Gerard Salton,et al.  Automatic Text Processing: The Transformation, Analysis, and Retrieval of Information by Computer , 1989 .

[67]  Daniel C. Berrios Automated indexing for full text information retrieval , 2000, AMIA.

[68]  Richard Fikes,et al.  The Ontolingua Server: a tool for collaborative ontology construction , 1997, Int. J. Hum. Comput. Stud..

[69]  Margaret King,et al.  Evaluating natural language processing systems , 1996, CACM.

[70]  K A Spackman,et al.  Recognizing noun phrases in medical discharge summaries: an evaluation of two natural language parsers. , 1996, Proceedings : a conference of the American Medical Informatics Association. AMIA Fall Symposium.

[71]  Lawrence M. Fagan,et al.  Automation and integration of components for generalized semantic markup of electronic medical texts , 1999, AMIA.

[72]  Wendy G. Lehnert,et al.  Using Decision Trees for Coreference Resolution , 1995, IJCAI.

[73]  Marius Fieschi,et al.  Model Formulation: UMLS-based Conceptual Queries to Biomedical Information Databases: An Overview of the Project ARIANE , 1998, J. Am. Medical Informatics Assoc..

[74]  Stephen B. Johnson,et al.  Generic queries for meeting clinical information needs. , 1993, Bulletin of the Medical Library Association.

[75]  Humphrey Sm Research on Interactive Knowledge-Based Indexing: The MedIndEx Prototype. , 1989 .

[76]  V. Yu,et al.  Antimicrobial Therapy and Vaccines , 1999 .

[77]  Anita Sundaram,et al.  Information Retrieval: A Health Care Perspective , 1996 .

[78]  E H Shortliffe,et al.  Contextual models of clinical publications for enhancing retrieval from full-text databases. , 1995, Proceedings. Symposium on Computer Applications in Medical Care.

[79]  P. Haug,et al.  Computerized extraction of coded findings from free-text radiologic reports. Work in progress. , 1990, Radiology.

[80]  Michael McGill,et al.  Introduction to Modern Information Retrieval , 1983 .

[81]  Q E Whiting-O'Keefe,et al.  The STOR clinical information system. , 1988, M.D. computing : computers in medical practice.

[82]  Wanda Pratt Dynamic organization of search results using the UMLS , 1997, AMIA.

[83]  Harry R. Tennant,et al.  Building Usable Menu-Based Natural Language Interfaces To Databases , 1983, VLDB.

[84]  S. G. Axline,et al.  Computer-based consultations in clinical therapeutics: explanation and rule acquisition capabilities of the MYCIN system. , 1975, Computers and biomedical research, an international journal.

[85]  D. Covell,et al.  Information needs in office practice: are they being met? , 1985, Annals of internal medicine.

[86]  Carol Friedman,et al.  Towards a comprehensive medical language processing system: methods and issues , 1997, AMIA.

[87]  David Fisher,et al.  Machine Learning of Text Analysis Rules for Clinical Records , 1999 .

[88]  Lawrence M. Fagan,et al.  Empirical Formulation of a Generic Query Set for Clinical Information Retrieval Systems , 2001, MedInfo.

[89]  T A Pryor,et al.  The HELP medical record system. , 1988, M.D. computing : computers in medical practice.

[90]  Jennifer Niederst Web Design in a Nutshell , 2001 .